TABLE 3.
Dimorphic TE (indels, absent or present) analyzed in this study.
| TE-ID # | Retroelement | Nearest Flanking (/) Gene(s) | Location within Genome Reference Ch38/hg38, Chr 6 (strand) | Distance between TE and gene loci, bp |
NCBI dbVar Curated Common SVs | 1000 genomes SVs DGVa estd214, estd219 | ||
| DRB1 | DQA1 | DQB1 | ||||||
| 1 | AluORF10 | C6orf10 | 32346003-32346314 (−) | 232,455 | 291,403 | 313,153 | nssv16196990 | esv3844276 |
| 2 | AluLTR12.DRB5 | DRB5 | 32494420-32494692 (−) | 84,077 | 142,714 | 164,775 | ||
| 3 | AluLTR12.DRB1 | 3′ of DRB1 | 32579821-32580132 (+) | 1,052 | 57,274 | 79,335 | ||
| 4 | AluDRB1 | 5′ of DRB1 | 32603572-32603844 (+) | 13,712 | 33,834 | 55,623 | nssv16191854 | esv3608598, esv3844294 |
| 5 | AluMER66 | 5′ of DQA1 | ∼32621979 (+) | 32,131 | 15,427 | 37,448 | ||
| 6 | AluDQA1(.a) | 5′ of DQA1 | 32625934-32626239 (−) | 36,086 | 11,472 | 33,228 | nssv16185199 | |
| 7 | AluDQA1(B) | 5′ of DQA1 | 32629720-32629999 (−) | 39,872 | 7,407 | 29,468 | ||
| 8 | AluMER90.DQA1 | 5′ of DQA1 | 32634001-32634251 (+) | 44,153 | 3,155 | 25,216 | nssv16196737 | |
| 9 | AluSx.SV1 | 3′ of DQA1 | 32647187-32647484 (+) | 57,339 | 3,535 | 11,983 | nssv16197586 | esv3608604 |
| 10 | AluHAL1ME | 3′ of DQA1 | 32652010-32652295 (+) | 62,162 | 14,604 | 7,172 | nssv16185138 | |
| 11 | AluDQB1 | 5′ of DQB1 | ∼32663914 (+) | 74,066 | 20,244 | 4,447 | nssv16191333 | |
| 12 | AluTHE1A.DQB1 | 3′ of DQB1 | 32673367-32673677 (+) | 83,520 | 29,697 | 4,985 | ||
| 13 | AluMT1 | 3′ of MTCO3P1 | ∼32689573/32690722 (−) | 99,725 | 45,902 | 21,190 | ||
| 14 | AluMT2 | 5′ of MTCO3P1 | 32699625-32699910 (+) | 109,777 | 55,954 | 31,242 | ||
| 15 | AluMT3 | 5′ of MTCO3P1 | 32703983-32704299 (+) | 114,135 | 60,312 | 35,600 | ||
| 16 | AluDQA2 | 5′ of DQA2 | ∼32740293 (+) | 150,445 | 96,622 | 71,910 | ||
| 17 | AluDOB2 | 3′ of DOB | 32781456-32781764 (−) | 191,608 | 137,785 | 113,073 | nssv16187057 | esv3608614 |
| 18 | AluDOB1 | 3′ of DOB | ∼32804316 (−) | 215,818 | 161,995 | 137,283 | ||
| 19 | AluDPB2 | 5′ DPB2 | 33125647-33125965 (+) | 535,799 | 481,976 | 457,264 | nssv16201287 | |
| 20 | AluSc8-AluJb | HCG24/COL11A2 | 33158148-33159074 | 568,300 | 514,477 | 489,765 | nssv16192244 | |
| 21 | SVA-BTN | C6orf10/BTNL2 | 32384189-32386122 (−) | 194,580 | 251,284 | 273,345 | monomorphic | |
| 22 | SVA-DRB4/HERV9 | DRB4 | DBB:3800882 3802512 (−) | 5,049 | 71,597 | 89,567 | ||
| 23 | SVA-DRB5 | 5′ of DRB5 | 32531532-32532999 (+) | 45,770 | 105,874 | 126,468 | nssv16197894 | |
| 24 | SVA-DRB1 | 5′ of DRB1 | 32594193-32596780 (−) | 4,345 | 40,626 | 62,687 | nssv16196260 | |
| 25 | SVA-DQB1 fragmented | 3′ of DQB1 | ∼32653260 (−) | 63,412 | 9,589 | 6,207 | ||
| 26 | SVA-DPA1 | 3′ of DPA1 | 33058946-33060797 (−) | 469,098 | 415,275 | 390,563 | nssv16182953 | esv3608619 |
| 27 | SVA-DAXX (harlequin) | 5′ of DAXX | 33357412-33358020 (−) | 767,564 | 713,741 | 689,029 | ||
| 28 | SVA-ZBTB9 (cheshire) | 3′ of ZBTB9 | 33485065-33486622 (−) | 895,217 | 841,394 | 816,682 | ||
| 29 | LTR22-DRB7/8 | DRB7/DRB8 | DBB:3786680-3787163 (+) | 21,578 | 87,443 | 21,578 | ||
| 30 | LTR14-DRB1 | 3′ of DRB5 | 32512830-32513385 (+) | 47,237 | 124,021 | 146,082 | ||
| 31 | LTR3-DRB3/5 | 32559719-32567345 (−) | 11,424 | 70,061 | 92,122 | |||
| 32 | LTR12-DRB6 | DRB5/DRB6 | 32547022-32548487 (−) | 30,282 | 88,919 | 110,980 | nssv16188969 | |
| 33 | LTR12/AluY-DRB1 | DRB1 | 32578751-32581032 (−) | 595 | 57,206 | 78,291 | nssv16194730/ | |
| 33 | LTR12/AluY-DRB1 | nssv16195291 | ||||||
| 34 | MER11-DRB1 | DRB1 | ∼32586373 (+) | 3,475 | 51,033 | 73,094 | ||
| 35 | MER90/MLT2/MER90 | 5′ of DQA1 | 32634949-32635931 (−/−/−) | 45,101 | 1,475 | 23,536 | ||
| 36 | LTR16-DQA1/DQB1 | DQA1/-DQB1 | 32652876-32653193 (−) | 63,028 | 9,205 | 6,274 | ||
| 37 | MER11-DQB1 | 3′ of DQB1 | 32655746-32656815 (−) | 65,898 | 12,075 | 2,652 | nssv16194796 | esv3608605 |
| 38 | LTR5.DQB1 | 3′ of DQB1 | 32657125-32658083 (−) | 62,277 | 13,454 | 2,342 | nssv16192810 | esv3608606 |
| 39 | LTR13-DQB1 | 5′ of DQB1 | ∼32667893 (+) | 78,045 | 24,222 | 490 | ||
| 40 | L1PA10-DQB1 | 5′ of DQB1 | 32674360-32677391 (2 +) | 84,512 | 30,689 | 5,977 | nssv16197816 | esv3608607 |
| 41 | LTR5-L1PA10-DQB1 | 5′ of DQB1 | ∼32676160 (2 +) | 86,512 | 32,689 | 7,977 | ||
| 42 | LHS1/Tig4-MT | MTCO3P1/DQB3 | 32708859-32709255 (−) | 119,011 | 65,188 | 40,476 | nssv16189788 | esv3844306 |
| 43 | LTR42-DOB | HLA-DOB | 32811165-32811646 (+) | 221,317 | 167,494 | 142,782 | nssv16198930 | esv3844312 |
| 44 | Indel Region A | DQB1/MTCO3P1 | ∼32687972-32688307 | 98,124 | 44,301 | 19,589 | ||
UCSC genome browser at https://genome.ucsc.edu was the source of the gene loci positions for HLA-DRB1 (6:32,578,769–32,589,848), HLA-DQA1 (6:32,637,406–32,643,671), and HLA-DQB1 (6:32,659,467–32,668,383) and listed TE positions in the table. NCBI dbVar: https://www.ncbi.nlm.nih.gov/dbvar/; 1,000 genomes SVs: - DGVa: https://www.ebi.ac.uk/dgva/. Dimorphic TEs are structural variants (SVs) or indels. TE-ID #20 noted but not analyzed (insufficient samples).Kulski et al. (2010), The 1000 Genomes Project Consortium et al. (2015a, b), Lee et al. (2020).